Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton

Abstract

Abstract Background Colored cotton is also called eco-cotton because of its natural color fiber. However, the yield and quality of natural colored cotton are generally lower than white cotton. Now, little is known about the regulatory mechanisms involved in biochemical and metabolic pathways and critical genes between fiber quality and pigment synthesis. The present study used a pair of brown cotton near-isogenic lines (brown cotton ‘Z1-61’ and white cotton ‘RT’) to determine the transcriptomic and proteomic data of fiber (ovule) at 0DPA, 10DPA, and 20DPA. Results Integration analysis of the two-omics data demonstrated that the differential proteins with the same expression trend in the adjacent developmental stages were significantly and positively correlated with fold change. Enrichment analysis of metabolic pathway revealed that Z1-61, enriched in fiber elongation genes related to a flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism and many more genes (proteins) are up-regulated. Short Time-series Expression Miner analysis inferred that up-regulated genes of Z1-61 were specifically involved in the metabolism of carbohydrates, energy, and lipid, suggesting that these pathways play an important role in fiber elongation and pigmentation. We further analyzed the 164 glycosyltransferases genes were predominantly expressed in the early stage of Z1-61 fiber elongation while they were predominantly expressed during the later period of RT fibers elongation. And 15 MYB-bHLH-WD40 triple complex genes and other transcription factor genes such as C2H2 (12), ERF (11), and NAC (7) were also preferentially expressed in Z1-61. Weighted correlation network analysis exhibited that fatty acid synthesis and energy metabolism were the active metabolic pathways in both cotton genotypes during fiber development. The 10 hub genes obtained from the final screening can be considered to play a critical role in the process of fiber pigment deposition while ensuring that fiber quality does not degraded. Conclusion This is the first complementary analyses of the transcriptome and proteome related with the quality of brown cotton fiber. Those studies can be understood as better playing a major role in fiber quality enhancement and pigmentation during fiber elongation.